Figure 1

Chikungunya virus is found in MARCO-expressing floor lymphatic endothelial cells in the draining lymph node at 8 hpi

A. UMAP projection shows the fraction of counts aligning to the CHIKV genome for the 8 hpi timepoint.

B. UMAP projection shows CHIKV+ cells (>0 CHIKV counts) for the 8 hpi timepoint.

C. CHIKV counts are shown for cell types with >50 cells for the 8 hpi CHIKV-infected sample.

D. The fraction of cells identified as CHIKV+ is shown for each cell type for the 8 hpi timepoint.

E, F. MARCO (E) or Madcam1 (F) expression is shown for fLECs for mock-infected cells and CHIKV-infected cells classified as either CHIKV low or CHIKV high. P values were calculated using a two-sided Wilcoxon rank-sum test with Bonferroni correction. In the boxplot, the central lines, the box limits, and the whiskers represent medians, the interquartile range (IQR), and min/max values that are not outliers, respectively. Outliers are shown as points and include any values that are more than 1.5× IQR away from the box.


Figure S1

CHIKV may target MARCO-expressing LECs for infection

CHIKV signal

A. UMAP projection shows annotated cell types for the 24 hpi timepoint.

B. UMAP projection shows CHIKV sgRNA ratio (sgRNA counts / 5’ counts) for the 24 hpi timepoint.

C. The fraction of cells identified as CHIKV-high is shown for each cell type for the 24 hpi timepoint.

D. CHIKV sgRNA ratio is shown for cells with >0 sgRNA counts and >0 5’ counts. Cell types with >10 cells are shown.

E. The correlation between CHIKV sgRNA ratio and QC metrics is shown for CHIKV-high cells.


Cell type annotation

A. The correlation between annotated LEC subsets and reference data is shown for the 8 hpi and 24 hpi timepoint.

B. The expression of select marker genes is shown for the 8 hpi and 24 hpi timepoints.


Figure 5

IN PROGRESS